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countland
View on CRAN: Click
here
Download and install countland package within the R console
Install from CRAN:
install.packages("countland")
Install from Github:
library("remotes")
install_github("cran/countland")
Install by package version:
library("remotes")
install_version("countland", "0.1.2")
Attach the package and use:
library("countland")
Maintained by
Church Samuel H.
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-08-17
Latest Update: 2022-08-17
Description:
A set of functions for applying a
restricted linear algebra to the analysis of
count-based data. See the accompanying preprint
manuscript: "Normalizing need not be the norm:
count-based math for analyzing single-cell data"
Church et al (2022)
This tool is specifically designed to analyze
count matrices from single cell RNA sequencing
assays. The tools implement several count-based
approaches for standard steps in single-cell
RNA-seq analysis, including scoring genes and cells,
comparing cells and clustering, calculating differential
gene expression, and several methods for rank
reduction. There are many opportunities for further
optimization that may prove useful in the analysis of
other data. We provide the source code freely
available at
and encourage users and developers to fork the code for
their own purposes.
How to cite:
Church Samuel H. (2022). countland: Analysis of Biological Count Data, Especially from Single-Cell RNA-Seq. R package version 0.1.2, https://cran.r-project.org/web/packages/countland. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.1.1 (2022-08-17 08:40)
Other packages that cited countland R package
View countland citation profile
Other R packages that countland depends,
imports, suggests or enhances
Complete documentation for countland
Functions, R codes and Examples using
the countland R package
Some associated functions: Center . Cluster . CountIndex . Dot . Embed . IMA . IMA_Compute_Init_Scaled . IMA_Update_Factor . IMA_init . IMA_params . Log . Normalize . PlotEigengap . PlotEmbedding . PlotGeneCounts . PlotIMA . PlotIMAElbow . PlotMarker . PlotSharedCounts . PrintGeneNumber . RankMarkerGenes . RemoveEmpty . RescaleVariance . RestoreCounts . RunIMA . ScikitManifoldSpectralEmbedding . ScoreCells . ScoreGenes . SharedCounts . Subsample . SubsampleCol . SubsetCells . SubsetGenes . countland-class . countland . listCols .
Some associated R codes: IMA.R . countland.R . countland_IMA.R . countland_cluster.R . countland_dot.R . countland_embed.R . countland_marker.R . countland_score.R . countland_shared_counts.R . countland_subsample.R . countland_subset.R . countland_utils.R . Full countland package functions and examples
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